SMTL ID : 3u2z.1

Activator-Bound Structure of Human Pyruvate Kinase M2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.1: 18 residues within 4Å: Chain A: L.433, T.434, K.435, S.436, R.438, S.439, W.484, R.491, T.515, G.516, W.517, R.518, P.519, G.520, S.521, G.522, F.523, T.524 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.435, A:S.436, A:G.437, A:S.439, A:S.439, A:S.439, A:G.516, A:R.518, A:R.518, A:G.520, A:S.521, A:G.522, A:F.523 Water bridges: A:R.491, A:R.491, A:T.524 Salt bridges: A:K.435, A:R.491 FBP.9: 18 residues within 4Å: Chain B: L.433, T.434, K.435, S.436, G.437, R.438, S.439, W.484, R.491, G.516, W.517, R.518, P.519, G.520, S.521, G.522, F.523, T.524 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:K.435, B:S.436, B:G.437, B:S.439, B:S.439, B:G.516, B:R.518, B:R.518, B:G.520, B:S.521, B:G.522, B:F.523, B:T.524 Water bridges: B:R.438, B:R.438, B:R.491, B:R.491 Salt bridges: B:K.435, B:R.491 FBP.15: 17 residues within 4Å: Chain C: L.433, T.434, K.435, S.436, R.438, S.439, W.484, R.491, T.515, G.516, R.518, P.519, G.520, S.521, G.522, F.523, T.524 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.434, C:K.435, C:S.436, C:G.437, C:S.439, C:S.439, C:G.516, C:G.520, C:S.521, C:G.522, C:F.523, C:T.524 Water bridges: C:R.491 Salt bridges: C:R.491 FBP.21: 17 residues within 4Å: Chain D: L.433, T.434, K.435, S.436, R.438, S.439, W.484, R.491, G.516, W.517, R.518, P.519, G.520, S.521, G.522, F.523, T.524 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:T.434, D:K.435, D:S.436, D:S.439, D:S.439, D:S.439, D:G.516, D:R.518, D:G.520, D:S.521, D:G.522, D:F.523 Water bridges: D:R.438, D:R.438, D:R.491, D:R.491 Salt bridges: D:K.435, D:R.491

21 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 6 residues within 4Å: Chain A: N.77, S.79, D.115, T.116, S.245, K.272 Ligand excluded by PLIP UNX.3: 2 residues within 4Å: Chain A: D.238, R.463 Ligand excluded by PLIP UNX.4: 3 residues within 4Å: Chain A: K.272, E.274, D.298 Ligand excluded by PLIP UNX.5: 6 residues within 4Å: Chain A: R.296, Q.312, D.349, N.352, A.353 Chain B: S.348 Ligand excluded by PLIP UNX.6: 1 residues within 4Å: Chain A: R.280 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: N.212, L.213, E.302 Ligand excluded by PLIP UNX.10: 2 residues within 4Å: Chain B: E.274, D.298 Ligand excluded by PLIP UNX.11: 4 residues within 4Å: Chain B: A.295, G.297, D.298, T.330 Ligand excluded by PLIP UNX.12: 7 residues within 4Å: Chain B: M.336, I.337, E.366, G.370, D.371, Y.372, P.373 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain B: P.55, R.58, Y.85 Ligand excluded by PLIP UNX.14: 6 residues within 4Å: Chain B: L.213, P.214, G.215, N.275, H.276, E.302 Ligand excluded by PLIP UNX.17: 3 residues within 4Å: Chain C: A.87, I.90, Q.237 Ligand excluded by PLIP UNX.18: 6 residues within 4Å: Chain C: N.77, S.79, D.115, T.116, S.245, K.272 Ligand excluded by PLIP UNX.19: 4 residues within 4Å: Chain C: F.246, K.272, E.274, D.298 Ligand excluded by PLIP UNX.20: 5 residues within 4Å: Chain C: A.295, R.296, G.297, D.298, T.330 Ligand excluded by PLIP UNX.22: 5 residues within 4Å: Chain D: N.46, H.466, Y.468, G.470, I.471 Ligand excluded by PLIP UNX.23: 4 residues within 4Å: Chain D: A.295, G.297, D.298, T.330 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain D: E.274, D.298 Ligand excluded by PLIP UNX.25: 7 residues within 4Å: Chain D: M.336, I.337, E.366, G.370, D.371, Y.372, P.373 Ligand excluded by PLIP UNX.26: 6 residues within 4Å: Chain D: T.97, E.98, Y.107, P.109, V.110, R.463 Ligand excluded by PLIP UNX.27: 3 residues within 4Å: Chain D: G.215, H.276, E.277 Ligand excluded by PLIP

2 x 07T: 6-(3-aminobenzyl)-4-methyl-2-methylsulfinyl-4,6-dihydro-5H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-5-one(Non-covalent)

07T.8: 12 residues within 4Å: Chain A: F.28, L.29, M.32, Y.392, Q.395, L.396 Chain B: F.28, D.356, Y.392, Q.395, L.396, E.399 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.29, B:L.396, B:L.396 Water bridges: A:Y.392 pi-Stacking: A:F.28, A:F.28, A:F.28, B:F.28, B:F.28 Hydrogen bonds: B:L.355 07T.16: 13 residues within 4Å: Chain C: F.28, L.29, M.32, I.391, Y.392, Q.395, L.396 Chain D: F.28, D.356, Y.392, Q.395, L.396, E.399 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:L.396, C:F.28, C:L.29 Hydrogen bonds: D:D.356 pi-Stacking: D:F.28, D:F.28, C:F.28, C:F.28, C:F.28 Water bridges: C:Y.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anastasiou, D. et al., Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis. Nat.Chem.Biol. (2012)

Release Date

2012-09-12

Peptides

Pyruvate kinase isozymes M1/M2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase isozymes M1/M2